From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Wed Jun 02 2004 - 16:04:15 CDT
Hello,
This error is very suggestive of incorrectly built system box. The atoms
are nearly on top of each other according to the VDW entry, and bonds seem
to be cut in half, making angle energies off the scale.
Recheck your box size and send your config file with psf and pdb files if
you need more help.
Brian
On Wed, 2 Jun 2004, Zhong Wenyu wrote:
> Hi.
> I have constructed a system contains lipid and DNA and carbon nanotube.The parameters files I used are par_all27_prot_lipid.inp and par_all27_na.inp. I meet some problems in minmization.
>
> TCL: Minimizing for 1200 steps
> PRESSURE: 0 nan nan nan nan nan nan nan nan nan
> GPRESSURE: 0 nan nan nan nan nan nan nan nan nan
> ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP TOTAL2 TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG
>
> ENERGY: 0 126435.5317 -99999999.9999 16158.4504 246.0499 -690784.5080 99999999.9999 0.0000 0.0000 0.0000 -99999999.9999 0.0000 -99999999.9999 -99999999.9999 0.0000 -99999999.9999 -99999999.9999 2906800.0000 -99999999.9999 -99999999.9999
>
> INITIAL STEP: 1e-06
> GRADIENT TOLERANCE: nan
>
> Then the computation hold on, neither stop nor continue work.
> Anyone could help me?
> Best regards.
>
> Wenyu Zhong
*****************************************************************
**Brian Bennion, Ph.D. **
**Computational and Systems Biology Division **
**Biology and Biotechnology Research Program **
**Lawrence Livermore National Laboratory **
**P.O. Box 808, L-448 bennion1_at_llnl.gov **
**7000 East Avenue phone: (925) 422-5722 **
**Livermore, CA 94550 fax: (925) 424-6605 **
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